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Items: 26

1.

Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance.

Bertolini JA, Favaro R, Zhu Y, Pagin M, Ngan CY, Wong CH, Tjong H, Vermunt MW, Martynoga B, Barone C, Mariani J, Cardozo MJ, Tabanera N, Zambelli F, Mercurio S, Ottolenghi S, Robson P, Creyghton MP, Bovolenta P, Pavesi G, Guillemot F, Nicolis SK, Wei CL.

Cell Stem Cell. 2019 Mar 7;24(3):462-476.e6. doi: 10.1016/j.stem.2019.02.004.

2.

Picky comprehensively detects high-resolution structural variants in nanopore long reads.

Gong L, Wong CH, Cheng WC, Tjong H, Menghi F, Ngan CY, Liu ET, Wei CL.

Nat Methods. 2018 Jun;15(6):455-460. doi: 10.1038/s41592-018-0002-6. Epub 2018 Apr 30.

3.

Producing genome structure populations with the dynamic and automated PGS software.

Hua N, Tjong H, Shin H, Gong K, Zhou XJ, Alber F.

Nat Protoc. 2018 May;13(5):915-926. doi: 10.1038/nprot.2018.008. Epub 2018 Apr 5.

4.

Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells.

Caridi CP, Delabaere L, Tjong H, Hopp H, Das D, Alber F, Chiolo I.

Methods Enzymol. 2018;601:359-389. doi: 10.1016/bs.mie.2017.11.033. Epub 2018 Feb 26.

5.

The three-dimensional genome organization of Drosophila melanogaster through data integration.

Li Q, Tjong H, Li X, Gong K, Zhou XJ, Chiolo I, Alber F.

Genome Biol. 2017 Jul 31;18(1):145. doi: 10.1186/s13059-017-1264-5.

6.

Electrostatic effects on the folding stability of FKBP12.

Batra J, Tjong H, Zhou HX.

Protein Eng Des Sel. 2016 Aug;29(8):301-308. doi: 10.1093/protein/gzw014. Epub 2016 Jul 5.

7.

Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities.

Dai C, Li W, Tjong H, Hao S, Zhou Y, Li Q, Chen L, Zhu B, Alber F, Jasmine Zhou X.

Nat Commun. 2016 May 31;7:11549. doi: 10.1038/ncomms11549.

8.

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization.

Tjong H, Li W, Kalhor R, Dai C, Hao S, Gong K, Zhou Y, Li H, Zhou XJ, Le Gros MA, Larabell CA, Chen L, Alber F.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):E1663-72. doi: 10.1073/pnas.1512577113. Epub 2016 Mar 7.

9.

Global reorganization of budding yeast chromosome conformation in different physiological conditions.

Dultz E, Tjong H, Weider E, Herzog M, Young B, Brune C, Müllner D, Loewen C, Alber F, Weis K.

J Cell Biol. 2016 Feb 1;212(3):321-34. doi: 10.1083/jcb.201507069. Epub 2016 Jan 25.

10.

TopDom: an efficient and deterministic method for identifying topological domains in genomes.

Shin H, Shi Y, Dai C, Tjong H, Gong K, Alber F, Zhou XJ.

Nucleic Acids Res. 2016 Apr 20;44(7):e70. doi: 10.1093/nar/gkv1505. Epub 2015 Dec 23.

11.

Comparative 3D genome structure analysis of the fission and the budding yeast.

Gong K, Tjong H, Zhou XJ, Alber F.

PLoS One. 2015 Mar 23;10(3):e0119672. doi: 10.1371/journal.pone.0119672. eCollection 2015.

12.

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast.

Tjong H, Gong K, Chen L, Alber F.

Genome Res. 2012 Jul;22(7):1295-305. doi: 10.1101/gr.129437.111. Epub 2012 May 22.

13.

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.

Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L.

Nat Biotechnol. 2011 Dec 25;30(1):90-8. doi: 10.1038/nbt.2057.

14.

Exploring the spatial and temporal organization of a cell's proteome.

Beck M, Topf M, Frazier Z, Tjong H, Xu M, Zhang S, Alber F.

J Struct Biol. 2011 Mar;173(3):483-96. doi: 10.1016/j.jsb.2010.11.011. Epub 2010 Nov 19. Review.

15.
16.

Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins.

Maniccia AW, Yang W, Johnson JA, Li S, Tjong H, Zhou HX, Shaket LA, Yang JJ.

PMC Biophys. 2009 Dec 21;2:11. doi: 10.1186/1757-5036-2-11.

17.

Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method.

Tjong H, Zhou HX.

J Chem Theory Comput. 2008 Oct 14;4(10):1733-1744. Epub 2008 Sep 6.

18.

Rational design of a conformation-switchable Ca2+- and Tb3+-binding protein without the use of multiple coupled metal-binding sites.

Li S, Yang W, Maniccia AW, Barrow D Jr, Tjong H, Zhou HX, Yang JJ.

FEBS J. 2008 Oct;275(20):5048-61. doi: 10.1111/j.1742-4658.2008.06638.x. Epub 2008 Sep 10.

19.

Spontaneous conformational change and toxin binding in alpha7 acetylcholine receptor: insight into channel activation and inhibition.

Yi M, Tjong H, Zhou HX.

Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8280-5. doi: 10.1073/pnas.0710530105. Epub 2008 Jun 9.

20.

Prediction of protein solubility from calculation of transfer free energy.

Tjong H, Zhou HX.

Biophys J. 2008 Sep 15;95(6):2601-9. doi: 10.1529/biophysj.107.127746. Epub 2008 May 30.

21.

On the Dielectric Boundary in Poisson-Boltzmann Calculations.

Tjong H, Zhou HX.

J Chem Theory Comput. 2008 Mar;4(3):507-514. Epub 2008 Feb 21.

22.

PI2PE: protein interface/interior prediction engine.

Tjong H, Qin S, Zhou HX.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W357-62. Epub 2007 May 25.

23.
24.

GBr(6): a parameterization-free, accurate, analytical generalized born method.

Tjong H, Zhou HX.

J Phys Chem B. 2007 Mar 22;111(11):3055-61. Epub 2007 Feb 20.

PMID:
17309289
25.

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.

Tjong H, Zhou HX.

Nucleic Acids Res. 2007;35(5):1465-77. Epub 2007 Feb 6.

26.

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